30 April 2008

Today was a bit of a strange day. It was the last day of class. There was free lunch to celebrate the university get re-accredited (even though this happened several months back). And then the chemistry department upstairs had more free food at the end of the day as their end of year celebration. Very bad, since habits learned in grad school -- when there's free food, you take it -- die very hard.

28 April 2008

The Austin Chronicle's Naked City blog comments on the recent announcement of Kenneth Heydrick as the science director for the Texas Education Agency:

The Texas Education Agency has offered the job of science coordinator to Kenn Heydrick. That should quash the conspiracy theorists who speculated that the agency removed former coordinator Chris Comer last year to replace her with someone who supports intelligent design.

Emphasis added.

It's a little premature to conclude that, "Evolution could not have been the reason for someone's dismissal, because the position was filled by someone supportive of teaching evolution." Let's not forget that Chris Comer's forced resignation attracted national news attention negative to the state of Texas, almost all of which was extremely negative. There was some in very strong advocacy from university professors on the part of teaching evolution. It is at least conceivable that some people in hiring positions noted this, and realized that hiring anyone with weak credentials or wishy-washy views on the subject of evolution would make a lot of people look very, very bad.

I started off my research career with octopuses when I was in a landlocked prairie province. And my supervisor talked from time to time about the deep mystery that cephalopods (squids, octopus, cuttlefish) could use colour, but couldn't see colour. So this is the sort of paper I've been waiting a long while to read.

To get a tiny little taste of the remarkable behaviour of these animals, check out David Gallo's talk below; the relevant bits start about 1 minute 50 seconds in.

I like to show the TED talk first, because it's so great to hear the audience's response. But if you want to see the last bit alone...

This new paper tests the idea that the colours that cuttlefish can make are similar enough to the colours found in their natural habitat that the animals don't need to see colour. That is, if you can change colour to many different shades of brown, you are not likely to stand out too much if you inhabit an area where most things are brown.

There's surprisingly little behaviour or physiology in this paper, which is unusual for this journal. The main technique the authors used was to photograph cuttlefish on various natural and artificial substrates. The digital revolution in photography is making feasible what would have been a nightmare not too long ago. It's now dead simple to take an image, put it into a computer, measure its red, green and blue values, brightness, and so on.

The team selected several spots on the cuttlefish body to measure the animal's colour, then selected several spots on the nearby substrate to measure the colour of the surrounding sand, shell grit, and so on. Some sand were commercially available sands that were... perhaps not quite natural looking (bright red), and others were collected nearby.

They then used computers to compare the cuttlefish colour and the surface. In general, it's quite a good match. Interestingly, however, the match seems to get better as the water gets deeper. If you've ever swam underwater, you know that colours change because the water filters out the light. Red light drops out really quickly, so the deeper you go, the more blue the water appears.

I had to say "seems to get better" in the previous paragraph, because the researchers didn't actually photograph in anything other than very shallow water. Instead, they calculated what they would expect to see at increasingly greater depths. Although I would normally grumble at this, the physics of light and water are probably sufficiently well understood by now that this is probably a pretty safe prediction.

The paper also presents some data on the colour pigments in the animal, but this basically confirms what people had seen by eye: there are three colours in the dorsal side of the animal, and two ventrally.

Thus, this paper hints that how to use colour while being colour blind is a problem with an evolutionary solution, rather than a physiological one. Those with the pigments that best match their local habitat will win out over generations, not in the few seconds where the animals are making those lightning fast colour changes.

Turning on the computer is typically one of the first things I do in the morning after having a shower. Yes, it's not a good habit. But this morning, I got rewarded for it.

I had just tweaked a lecture for my general biology students last night, and I knew what I was going to talk about. This was my last lecture for the semester. I had talked about viruses last week, and was going to talk about how molecules originally discovered in viruses (integrase and reverse transcriptase) were now being used in biotechnology applications, including gene therapy.

The headline is a bit over the top (the patients weren't completely blind, for instance), but the science was exactly what my lecture (in a couple of hours) was about: using a virus to deliver a modified gene to a patient. And the article even has an associated video showing some of the behavioural trials with the patients.

I love being able to bring in that newly published stuff into my class, but sadly, it's rare that you have the opportunity to do so, particularly in a general introductory class. So this was just friggin' awesome, and a great way to drive home the point that this is a great time to be studying biology.

26 April 2008

The press release says that he has edited a biology textbook, though I can't find what it is, and that his first degree is in biology. Even more encouraging, an Austin American-Statesman Homeroom blog notes:

Heydrick has stood up to attempts to weaken teaching evolution in the past, asking the State Board of Education in a 2003 hearing on textbooks not to require changes in textbooks to water-down evolution lessons or add “nonscientific alternatives such as intelligent design.”

Heydrick, who worked as a high school science teacher for 10 years, has held several state and national leadership positions, serving as immediate past president of the Science Teachers Association of Texas and on the State Board of Education's earth science task force.

I can't resist quoting a snipe from the American-Statesman blog, though:

And his current boss at Pflugerville says he’s good at working with teachers and working with others, plus he’s got seven dogs and four cats. Because being an animal lover obviously makes him better qualified to shape the state science curriculum.

Ha!

This appears to be good news on the face of it. Certainly, there had to be the worry on whether the TEA would try to hire someone with weak credentials in biology. But he appears to have the chops.

Two major antievolution stories in Texas are ending on an optimistic note in the same week. Interesting.

24 April 2008

The Houston Chronicle was one of the first news organizations to confirm what's already been on the blogosphere: that THECB denied ICR's MS in science education plans. A follow-up story notes there was little discussion before the vote, probably due to the public presentations made before the earlier committee vote.

The news services have been reasonably quiet about this decision.

So far, almost the only editorial comment I've seen has been from the Austin American Statesman, which wrote:

Dedicated learning in its many forms is generally wonderful. But course work must be labeled correctly. The state is right to require that a graduate degree in creation studies, which the Institute of Creation Research offers, be called what it is - a degree in religion, not science. ... Paredes and the coordinating board took a correct and principled stand in denying the creationist institute’s science course.

Meanwhile, the Daily Skiff blog from Texas Christian University reports on the ICR's press release following the decision against them:

The manner in which the hearing was conducted was characterized by viewpoint discrimination.

I wonder what "viewpoint discrimination" is. Is it something different than disagreeing?

The Texas Observer noted that there were three people who spoke in favour and seven who opposed it. If there was nobody who spoke in favour, or only one, that might be a stronger case for not having a chance to make the case.

It could also just point out that many people think that the program as proposed is just a bad idea.

The Texas Observer blog is reporting that the Texas Higher Education Coordinating Board (THECB) supported the Academic Excellence Committee's recommendation: No science education Master's for the Institute for Creation Research (ICR).

I'm waiting to see more news coverage, but if so, this would spell the end of the main event. But given that several news stories have mentioned that ICR will follow "due process," expect a rematch.

Nature blog The Great Beyond comments briefly about the THECB committee recommendation.

And finally, the Texas Freedom Network had a press release about survey results of Texas university faculty on the ICR issue. Science faculty were against the idea.

The following is a blog post I made over at the All in the Mind blog in response to a recent show on evolutionary psychiatry. I wanted to post it here, because I've been wanting to discuss the "reptilian brain" idea for some time, as it may well be one of the most popular but wrong ideas about the evolution of nervous systems out there.

More posts on reptile brains later, I hope.

;;;;;

The basic premise discussed in this show -- that human behaviour has an evolutionary history -- is not terribly contentious. The specific model discussed in the program, Paul MacLean's "triune brain," is more problematic.

As typically expressed, MacLean's model suggests that entire reptilian brain has been conserved through the evolution of the mammals, with new brain regions essentially added on to the existing core, like suburbs being added to a city.

There are a few problems with this model.

First, MacLean's ideas seem to be highly influenced by old ideas that emphasized the "march of progress" or the "great chain of being." In particular, the MacLean model seems to be based on the notion that reptiles were the ancestors of mammals. It's debatable whether reptiles are the ancestors of mammals, however. It may be that the two groups shared a common ancestor, then diverged. It's also somewhat misleading in that it lumps all reptiles together. Snakes, for instance, appear much later in the fossil record than the earliest mammals.

Second, the suggestion that the entire reptile brain is essentially the mammalian hind brain is not supported by modern neuroanatomy. To give an example, in MacLean's model, the limbic system is characterized as a "lower mammalian" part of the brain. There is evidence, however, that reptiles have a limbic system (Bruce and Neary, 1995; Lanuza et al., 1998).

MacLean's "triune brain" hypothesis may have caught the popular imagination, but it has not proved useful in modern neurobiology.

References

Bruce LL, Neary TJ. 1995. The limbic system of tetrapods: A comparative analysis of cortical and amygdalar populations. Brain, Behavior and Evolution46(4-5): 224-234.

More coverage this morning about the THECB's Academic Excellence Committee's recommendation in anticipation of the full Coordinating Board vote today.

The Houston Chronicle has an article that describes some of the testimony before the Committee vote:

Paredes' recommendation and the vote by members of the Academic Excellence and Research Committee followed a 30-minute public hearing, during which 10 people — most of whom said they held doctoral degrees in a scientific field — split over the issue.

"What they are calling science education has as much to do with science as reality television has to do with reality," said Paul Murray, a geophysicist from Austin.

Chris Krosschell, a former Air Force pilot, played a tape of Apollo 8 commander Frank Borman, speaking as he looked back at the Earth.

"In the beginning, God created the heavens and the earth," Borman said, quoting the opening passages of Genesis.

23 April 2008

The Austin American-Statesman has a longer story on the THECB committee vote, including pinpoint accurate comments from Ray Paredes (emphasis added):

Paredes said the institute's catalog and other records portray as unshakable fact that the Earth is about 6,000 years old, that God created all things in the universe in six days as described in Genesis, that theories of origin and development involving evolution are false, and that most biblical miracles require a temporary suspension of basic natural laws.

"Whatever the ultimate merit of such views, they clearly stand at odds with the most basic tenets of scientific work such as observation, testing and analysis," Paredes said.

A lawyer for the Bible-based group also warned that the coordinating board could eventually face legal action for suppressing the free-speech rights of the institute.

THECB commissioner Ray Paredes is quoted:

“Evolution is such a fundamental principle of contemporary science it is hard to imagine how you could cover the various fields of science without giving it [evolution] the proper attention it deserves as a foundation of science,” he said.

I feel bad about the carbon footprint (stupid infrastructure determining my choices again), but I am happy with why: I finally was able to go out to the Coastal Studies Lab and get some data that will help wind up some experiments my student and I started back in December or so with some shrimp.

If you've ever wanted to imitate a scientist, just watch the picture below for 10 minutes.

Okay, now do that 14 more times.

The shrimp were pretty subdued and didn't do a tremendous amount of behaving for me. Which, in the context of the experiment, is actually interesting.

"We have been told second-hand, through our contact, that their objection is that we are using the word 'science.' If we would just drop the word science," the approval would go through, said Morris.

Which raises the question of why they don't simply call it a degree in creation studies and be done with it. That would seem to be the "everyone wins" scenario. ICR gets their program with an honest label.

He argued that students exercise critical thinking skills when they are taught how to compare an evolutionary mindset to a creationist mindset.

"How can you be a critical thinker if you don't know what the other side is?" he asked.

Saying you are "the other dies" does not make that side equally valid. Even if it was, you have to have some confidence that alternate views are treated objectively. And the Institute of Creation Research has made it very clear that it's anti-evolution, and it does not represent the consensus view on science. It's fringe.

Regardless of the outcome this week, this is unlikely to be over this week...

The ICR has the option to appeal within 45 days and/or to reapply within 180 days if the Board rejects the application. In the case of approval, ICR will begin its effort to obtain accreditation from the Southern Association of Colleges and Schools.

16 April 2008

In case you saw the recent news story that a teenager corrected NASA about the probability of an asteroid impact... check here.

Besides, arguing about correct probilities over something like asteroid impacts seem to have a certain... I don't know... squishiness to it. It's not something that is going to have a definite answer, like the probability of throwing snake eyes in dice. It's going to be complex, and low probability, and highly subject to revision anyway.

Apparently, there's also been another story circulating in the US about a teenager who is doubting that climate change is caused by human burning of fossil fuels (no link now).

What is the point of such stories? In neither case is the teen rebel providing any sort of definitive evidence. They're getting press just for doubting at a slightly more sophisticated level than their peers. I'm glad they're interested in science, but shouldn't they get attention when, you know, they contribute actual data? Like all the rest of us professionals?

15 April 2008

I really like this post over at the DrugMonkey blog about the role of authority in science. I like it even though it has South Park pictures in it, which I detest.

Near the end, the talk turns to university instructors:

Your whole professional life is predicated on you as the Authority. In the classroom, you have all the knowledge and the students have relatively little. They are explicitly seeking you out for your authority. Even within most “teaching departments” you are the sole expert in not just a narrow area but in several subfields, are you not? And...c’mon, ‘fess up. It goes to your head after awhile doesn't it? ...

Is it any wonder you develop into a know-it-all who cannot conceptualize anyone else having valid opinions or rationales? Any wonder you start to broaden the scope of your claimed authority? After all, nobody challenges you in your day to day life. And for the most part, you are right. But not all the time, my friend, not all the time.

I think this is one of the reasons that extreme deference in my students drives me absolutely insane. I hope that at some level, I want to be challenged.

Having authority should mean recognizing challenges as challenges (in the best sense of the word) , not threats.

This video of Chris Comer describing her firing is up at an National Center for Science Education website devoted to the film Expelled. I haven't been blogging about Expelled, because many, many people have repeatedly identified it as a highly suspicious propaganda film. Not all that much to add there.

No new information there, really, but worthwhile to hear the story from Ms. Comer.

Also, the position she used to hold at the Texas Education Agency is still showing as vacant.

One of the things I occasionally get in my mailbox is updates from the National Science Foundation, since it is the agency that I look to most and have worked with most for funding. This morning, a link to a report about the NSF's "human capital" came in. I thought it was about science careers generally, but it turns out to be very specific to NSF employment. I did catch one interesting point:

While NSF’s workforce has grown by eight percent between 2001-2007, during that same time period, proposals submitted to NSF for competitive review grew 40 percent.

So, as expected, more and more people are looking for a piece of a pie that isn't getting any much bigger in a hurry.

Only nine days to go until the Institute for Creation Research's application to grant Master's degrees in science education is taken up by the Texas Higher Education Coordinating Board. It's on the agenda for the 24 April meeting. Item IX.H.

14 April 2008

You may be wondering about the local reaction to stories like this one:

The Bush administration is bulldozing environmental laws to build a controversial fence designed to block illegal immigrants from crossing the Mexican border. ... In southern Texas the fence will run along flood-control levees between 100 and 1500 metres from the Rio Grande, creating what critics call a "no-man's land" between fence and river.

This section of the fence will cut through rich wildlife reserves, including the Santa Ana National Wildlife Refuge in Alamo, the Sabal Palm Audubon Center and most of the Nature Conservancy's Lennox Foundation Southmost Preserve near Brownsville.

And it may surprise you that there really isn't much local reaction. I've seen occasional posters around campus saying "No border wall," but they're rare.

Additional: Of course, I write something like this and then discover there's going to be a forum about the fence held on campus tomorrow. Still, as I said, it's been very low key promotion.

10 April 2008

Earlier this week, I was involved in reviewing a proposal for a new textbook aimed at introductory biology students. The book was trying some different things in the way it was structured, and was trying to integrate mathematics throughout. All very smart, well-meaning stuff. But sometimes, you wonder if textbook authors forget the conditions on the ground.

Last week, I had a student come into my office who reminded me. He said he had been in the wrong class for the last two and a half months. He asked if he could make up the missing work.

Now, I had better provide a little context. I teach three classes in a row. Originally, I was slated to be in one room for the first class, then move down the hall for the next two. This seemed silly, so I asked the lecturer down the hall at the time of my first class if we could switch. That was fine. Signs on the doors of both classes were up for many weeks explaining that the class had moved.

The student had a class list at the start of the semester that listed all the rooms, and followed it. The printed list he had was not updated with the room switch.

The class he had been sitting in since the beginning of the semester wasn't even a biology class. Not even in the same discipline as class he was supposed to be taking.

(One person refused to believe this student's explanation. To which I replied, "If that's the story this person said to look good, what's the real story going to be like?")

I want to make something clear here: I am not laughing at these students. The point is that such students remind me that all the time I spend thinking about how to better explain gamete formation... or how to better use clickers... or to integrate quantitative mathematical into my lectures... is just not going to matter for a lot of students.

I just don't know that I can do anything to make it right for those people.

The BBC is reporting on this wonderful fossil. (There's a video here.) This is an old finding I wasn't previously aware of, but it's great to see how technology is getting ever better at making the unseen seen. The BBC link seems to indicate this will be appearing in the French journal Comptes Rendus Biologies.

09 April 2008

Just like cloning mammals arrived sooner than most people expected and left people scrambling for how to deal with the situation, I'm starting to think that we'd better start doing some serious thought about the legal ramifications of robotics.

I'm thinking much the same thoughts after reading this story and accompanying video.

To me, it's no surprise that people will respond emotionally to robots, because people tend to treat everything as alive. Watch the amount of attention people give to their cars sometime. I can't remember if I blogged about it, but I saw some time ago an interview with a researcher who found that the further people were from their computers, the more likely they were to use profanity in describing it -- that is, they were being polite to the computer.

Theodor Boveri was a developmental biologist, who did some important early work on cell division using Ascaris, a species of parasitic nematode worm. I wasn't familiar with his work, but scanned this recent review article.

The article ends saying that Boveri actually became infected with these parasites late in life, leading him to write:

It is mean when the beasts you have worked on, now start working on you.

08 April 2008

At lunch today, we official (re) installed a chapter of Beta Beta Beta in my department. This is a national honor's society for biology, which support undergraduate student academic success and undergraduate researchers.

Being Canadian, where the practice of fraternities and sororities has never been strong on universities, I had a certain suspicion about a society with so many Greek letters in it. But the students wanted a chapter, and I wanted to support the students, so I said I would be the advisor for the chapter and help get them off the ground.

So we had Ron Humphery, the regional director, down to officially start the chapter. It turned out that this was bringing a chapter back to our institution. We had a chapter way back in the 1980s, apparently -- our tech Tom was a member back then. But somehow, it lapsed and there hasn't been one for a long, long time.

Dr. Humphrey was actually a little surprised by how much the national office sent down for our new chapter, particularly a huge tablecloth with the Beta Beta Beta seal, which made the various bits on display (the charter for the chapter, the coat of arms, membership book, candles, etc.) look pretty darn classy.

And now we are chapter Nu Omega, with a few new members and high hopes. We'll see how it goes.

There's a new talk by Al Gore on TED today. I found it very interesting, particularly the analyses of where climate change sits on the food chain of the media.

Then my eyes strayed down to the comments.

Wow.

You hear about terms like "culture war" bandied about, and sometimes you wonder, "How bad is it really?" And then you see the absolute opposition, catcalling, insults, and appeals to conspiracy and cultism in something like this. Which, I have to point out, is about a topic that isn't scientifically controversial.

I think maybe Jimmy Wales got it right. The real culture war isn't over politics: "It's between the party of the thoughtful and the party of the jerks."

In this age of comments, reviews, and all of that which is supposed to be part of Web 2.0, the maddening thing is how easy it is to be a jerk. To hop onto a site and give a one start review with a one line dismissal to a book you've never read. And it creates such a caustic environment. Who wants to stand in the middle of a yelling contest?

And as much as I want to be one of the people reaching out to talk about science and education and my profession, seeing the jerks in action make me worry of getting burned.

Additional: And this is why comments here are moderated, incidentally.

07 April 2008

The peacock's tail is the example of a feature that seems to have evolved not for survival, but for attracting mates. And it is truly spectacular, as the video clip shows.

One explanation for the great size of the tail is that if females prefer mating with males with large tails, those males will have greater reproductive success. Thus, there will be selection for the large spectacular tails that peacocks have.

This paper is getting a fair amount of attention (e.g., a mention on the latest Science podcast) because it counter intuitively argues that females do not prefer males with larger tails.

There's something important to know about this paper: The authors didn't do any experiments. That is, they never actually changed the tails of males in any way to see if this changed their courtship or mating success.

Instead, they watched peacocks and peahens mating in a free-ranging population in Japan (268 matings, if you're curious), and measured the peacocks' tails in various ways from photographs. Then, they looked to see if there were any correlations between tail shape and mating success.

No correlation between the length of the tail and mating success.

No correlation between the number of eyespots on the tail and mating success.

And this is where this being a study rather than an experiment makes the interpretation difficult. The authors worked simply with what they found in their field setting. And there was very little variation in peacock tails. If there's no variation, it's very difficult to make any conclusions about choice.

Image a situation where you have to pick between numerous $1 bills. You pick a $1 bill more or less at random, and the researcher concludes that value plays little role in your decision making process. The peahens may not have had much to distinguish the peacocks here, so other factors may become more important.

Indeed, the authors found correlations between behaviour called "shivering" and mating success. When the authors put all these factors to try to explain mating success in a single year, however, not much is explained.

They also found a correlation between tail length and predation -- although few peacocks were preyed upon. Although many individuals were identified using leg bands, the authors say very little about the age of the individuals they were studying. One could image a situation where the oldest mails have the longest tails, but because they are old, they are the most vulnerable to predators.

The authors propose that the peacock's tail is a relic. That is, it was important once, but is mostly unimportant now. This is an interesting idea, as are several others that they float in the discussion. But ultimately, I wish they had done some experiments.